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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(print,tagMepprIndex)
S3method(print,tagMepprSample)
S3method(results,tagMepprSample)
export(align)
export(checkPrimer)
export(findInsertions)
export(loadIndex)
export(makeIndex)
export(newTagMeppr)
export(plotInsertions)
export(plotSite)
export(results)
export(runIDgen)
export(tagMepprCol)
importFrom(BSgenome,getSeq)
importFrom(BSgenome.Hsapiens.UCSC.hg19,BSgenome.Hsapiens.UCSC.hg19)
importFrom(BiocGenerics,end)
importFrom(BiocGenerics,start)
importFrom(BiocGenerics,strand)
importFrom(Biostrings,DNAString)
importFrom(Biostrings,letterFrequency)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,vmatchPattern)
importFrom(Biostrings,writeXStringSet)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqnames)
importFrom(GenomicAlignments,readGAlignments)
importFrom(GenomicAlignments,width)
importFrom(GenomicRanges,GRanges)
importFrom(GenomicRanges,GRangesList)
importFrom(GenomicRanges,as.data.frame)
importFrom(GenomicRanges,countOverlaps)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,strand)
importFrom(IRanges,IRanges)
importFrom(IRanges,coverage)
importFrom(IRanges,subsetByOverlaps)
importFrom(Rsamtools,ScanBamParam)
importFrom(S4Vectors,mcols)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,runValue)
importFrom(S4Vectors,subjectHits)
importFrom(S4Vectors,width)
importFrom(dplyr,bind_rows)
importFrom(dplyr,full_join)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expand_scale)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_polygon)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(metap,sump)
importFrom(reshape2,colsplit)
importFrom(rtracklayer,export.bed)
importFrom(rtracklayer,import.bed)
importFrom(scales,extended_breaks)
importFrom(scales,hue_pal)
importFrom(stats,approx)
importFrom(stats,complete.cases)
importFrom(stats,p.adjust)
importFrom(stats,setNames)
importFrom(utils,read.delim)
importFrom(utils,write.table)